make Speroid file also work with relative paths

Author: rgerum

saenopy/gui/common/gui_classes.py

@@ -302,7 +302,7 @@ def __init__(self, layout, editable=False, add_item_button=False, color_picker=F
         self.customContextMenuRequested.connect(self.list2_context_menu)
         self.itemChanged.connect(self.list2_checked_changed)
         self.itemChanged = self.itemChanged2
-        self.act_delete = QtWidgets.QAction(qta.icon("fa.minus"), "Remove", self)
+        self.act_delete = QtWidgets.QAction(qta.icon("fa5s.minus"), "Remove", self)
         self.act_delete.triggered.connect(self.delete_item)
 
         self.act_color = None

saenopy/gui/spheroid/modules/DeformationDetector.py

@@ -22,6 +22,7 @@ class DeformationDetector(PipelineModule):
     pipeline_name = "find deformations"
     use_thread = False
     progress_signal = QtCore.Signal(int, str)
+    result: ResultSpheroid = None
 
     def __init__(self, parent: "BatchEvaluate", layout):
         super().__init__(parent, layout)
@@ -232,7 +233,7 @@ def update_display(self, *, plotter=None):
         if self.show_seg.value():
             thresh_segmentation = self.thresh_segmentation.value()
             if not self.continuous_segmentation.value():
-                im0 = imageio.v2.imread(self.result.images[0]).astype(float)
+                im0 = imageio.v2.imread(self.result.get_image_data(0, return_filename=True)).astype(float)
             seg0 = jf.piv.segment_spheroid(im0, True, thresh_segmentation)
             from skimage import measure
             # Find contours at a constant value of 0.8

saenopy/gui/spheroid/modules/path_editor.py

@@ -4,9 +4,10 @@
 
 from saenopy.gui.common import QtShortCuts
 from saenopy.gui.solver.modules.path_editor import PathChanger
+from saenopy.gui.spheroid.modules.result import ResultSpheroid
 
 
-def start_path_change(parent, result):
+def start_path_change(parent, result: ResultSpheroid):
     path_editor = PathEditor(parent, result)
     if not path_editor.exec():
         return

saenopy/gui/spheroid/modules/result.py

@@ -9,7 +9,7 @@
 import matplotlib.pyplot as plt
 
 from saenopy.saveable import Saveable
-from saenopy.result_file import make_path_absolute
+from saenopy.result_file import make_path_absolute, make_path_relative
 
 
 
@@ -70,11 +70,30 @@ def __init__(self, template, images, output, **kwargs):
 
         super().__init__(**kwargs)
 
-    def save(self, file_name=None):
-        if file_name is None:
-            file_name = self.output
+    def save(self, filename: str = None):
+        if filename is None:
+            self.template = make_path_absolute(self.template, Path(self.output).parent)
+            for i in range(len(self.images)):
+                self.images[i] = make_path_absolute(self.images[i], Path(self.output).parent)
+
+            filename = self.output
+
+            self.template = make_path_relative(self.template, Path(self.output).parent)
+            for i in range(len(self.images)):
+                self.images[i] = make_path_relative(self.images[i], Path(self.output).parent)
         Path(self.output).parent.mkdir(exist_ok=True, parents=True)
-        super().save(file_name)
+        super().save(filename)
+
+    def on_load(self, filename: str):
+        self.template = make_path_relative(self.template, Path(self.output).parent)
+        for i in range(len(self.images)):
+            self.images[i] = make_path_relative(self.images[i], Path(self.output).parent)
+
+        self.output = str(Path(filename))
+
+        self.template = make_path_absolute(self.template, Path(self.output).parent)
+        for i in range(len(self.images)):
+            self.images[i] = make_path_absolute(self.images[i], Path(self.output).parent)
 
     def get_absolute_path(self):
         return make_path_absolute(self.template, Path(self.output).parent)
@@ -101,9 +120,11 @@ def get_data_structure(self):
             }
         }
 
-    def get_image_data(self, time_point, channel="default", use_reference=False):
+    def get_image_data(self, time_point, channel="default", use_reference=False, return_filename=False):
         try:
-            im = imread(self.images[time_point])
+            if return_filename:
+                return make_path_absolute(self.images[time_point], Path(self.output).parent)
+            im = imread(make_path_absolute(self.images[time_point], Path(self.output).parent))
         except FileNotFoundError as err:
             traceback.print_exception(err)
             h = 255

saenopy/gui/tfm2d/modules/result.py

@@ -144,6 +144,9 @@ def save(self, file_name=None):
         Path(self.output).parent.mkdir(exist_ok=True, parents=True)
         super().save(file_name)
 
+    def on_load(self, filename: str):
+        self.output = str(Path(filename))
+
     def get_mask(self):
         if self.mask is None:
             self.mask = get_mask_using_gui(self.bf)

saenopy/result_file.py

@@ -1,6 +1,7 @@
 import glob
 import re
 from pathlib import Path
+from pathlib import PurePath, PureWindowsPath
 import os
 import natsort
 from typing import List
@@ -227,21 +228,35 @@ def common_start(values):
             start = start[:-1]
 
 
-def make_path_relative(template, output):
-    template = str(Path(template).absolute())
-    output = str(Path(output).absolute())
-    # relative and optionally go up to two folders up
-    try:
-        template = Path(template).relative_to(output)
-    except ValueError:
-        try:
-            template = Path("..") / Path(template).relative_to(Path(output).parent)
-        except ValueError:
-            try:
-                template = Path("../..") / Path(template).relative_to(Path(output).parent.parent)
-            except ValueError:
-                pass
-    return str(template)
+def make_path_relative(filename, base):
+    """
+    Returns the relative path of `filename` with respect to the `base` directory,
+    working cross-platform for Windows paths on non-Windows systems.
+
+    :param filename: The path of the file.
+    :param base: The base directory to which the path should be relative.
+    :return: The relative path of the file.
+    """
+    # Convert to PurePath for cross-platform compatibility
+    base_path = PurePath(base)
+    file_path = PurePath(filename)
+
+    # Use PureWindowsPath if on a non-Windows system handling Windows paths
+    if not isinstance(base_path, PureWindowsPath) and '\\' in str(base):
+        base_path = PureWindowsPath(base)
+    if not isinstance(file_path, PureWindowsPath) and '\\' in str(filename):
+        file_path = PureWindowsPath(filename)
+
+    if not file_path.is_absolute():
+        return file_path
+
+    offset = ""
+    for i in range(3):
+        if file_path.is_relative_to(base_path):
+            return str(offset / file_path.relative_to(base_path))
+        base_path = base_path.parent
+        offset /= PurePath("..")
+    return file_path
 
 
 def make_path_absolute(template, output):